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References from Deep learning methods in protein structure prediction. Local targets link to admitted publications; unresolved targets remain external evidence.
Structure of myoglobin: a three-dimensional Fourier synthesis at 2 A. resolution
10.1038/185422a0 · 1960 · External reference
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Function and structure of inherently disordered proteins
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10.1093/bioinformatics/bth195
10.1093/bioinformatics/bth195 · External reference
Improved disorder prediction by combination of orthogonal approaches
10.1371/journal.pone.0004433 · 2009 · External reference
Predisorder: ab initio sequence-based prediction of protein disordered regions
10.1186/1471-2105-10-436 · 2009 · External reference
Espritz: accurate and fast prediction of protein disorder
10.1093/bioinformatics/btr682 · 2011 · External reference
Cspritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs
10.1093/nar/gkr411 · 2011 · External reference
10.1093/bioinformatics/btw446
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Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks
10.1093/bioinformatics/btw678 · 2017 · External reference
RaptorX-Property: a web server for protein structure property prediction
10.1093/nar/gkw306 · 2016 · External reference
10.1002/prot.21075
10.1002/prot.21075 · External reference
A comprehensive overview of computational protein disorder prediction methods
10.1039/c1mb05207a · 2012 · External reference
Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions
10.1007/s00018-017-2555-4 · 2017 · External reference
Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information
10.1186/1471-2105-8-201 · 2007 · External reference
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Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks
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10.1093/bioinformatics/btu352
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Deeper profiles and cascaded recurrent and convolutional neural networks for state-of-the-art protein secondary structure prediction
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Unresolved reference
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Uniprot: a hub for protein information
10.1093/nar/gku989 · 2014 · External reference
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10.1038/323533a0 · 1986 · External reference
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Predicting the secondary structure of globular proteins using neural network models
10.1016/0022-2836(88)90564-5 · 1988 · External reference
Protein secondary structure prediction with a neural network
10.1073/pnas.86.1.152 · 1989 · External reference
Predicting surface exposure of amino acids from protein sequence
10.1093/protein/3.8.659 · 1990 · External reference
Unresolved reference
2016 · External reference
10.1109/5.726791
10.1109/5.726791 · External reference
Finding structure in time
10.1207/s15516709cog1402_1 · 1990 · External reference
Learning long-term dependencies with gradient descent is difficult
10.1109/72.279181 · 1994 · External reference
10.1162/neco.1997.9.8.1735
10.1162/neco.1997.9.8.1735 · External reference
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10.3115/v1/w14-4012 · External reference
Exploiting the past and the future in protein secondary structure prediction
1999 · External reference
10.1109/cvpr.2016.90
10.1109/cvpr.2016.90 · External reference
10.1016/s0022-2836(64)80232-1
10.1016/s0022-2836(64)80232-1 · External reference
10.1021/bi00699a002
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Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure
10.1016/0022-2836(74)90404-5 · 1974 · External reference
Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
10.1016/0022-2836(78)90297-8 · 1978 · External reference
How good are predictions of protein secondary structure?
10.1016/0014-5793(82)80597-8 · 1983 · External reference
10.1006/jsbi.2001.4336
10.1006/jsbi.2001.4336 · External reference
10.1016/0022-2836(87)90189-6
10.1016/0022-2836(87)90189-6 · External reference
Prediction of protein secondary structure at better than 70% accuracy
10.1006/jmbi.1993.1413 · 1993 · External reference
10.1016/s0959-440x(96)80056-x
10.1016/s0959-440x(96)80056-x · External reference
10.1006/jmbi.1999.3091
10.1006/jmbi.1999.3091 · External reference
Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning
10.1038/srep11476 · 2015 · External reference
10.1101/289033
10.1101/289033 · External reference
10.1093/bioinformatics/btx218
10.1093/bioinformatics/btx218 · External reference
NetSurfP- 2.0: improved prediction of protein structural features by integrated deep learning
10.1002/prot.25674 · 2019 · External reference
Protein secondary structure prediction using nearest-neighbor methods
10.1006/jmbi.1993.1464 · 1993 · External reference
Exploring the limits of nearest neighbour secondary structure prediction
10.1093/protein/10.7.771 · 1997 · External reference
New method for accurate prediction of solvent accessibility from protein sequence
2000 · External reference
HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins
10.1006/jmbi.2000.3837 · 2000 · External reference
Protein backbone angle prediction with machine learning approaches
10.1093/bioinformatics/bth136 · 2004 · External reference
Better prediction of protein contact number using a support vector regression analysis of amino acid sequence
10.1186/1471-2105-6-248 · 2005 · External reference
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Protein secondary structure prediction with dihedral angles
10.1002/prot.20435 · 2005 · External reference
10.1002/prot.10082
10.1002/prot.10082 · External reference
Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
10.1093/bioinformatics/18.suppl_1.s62 · 2002 · External reference
10.1093/bioinformatics/bti203
10.1093/bioinformatics/bti203 · External reference
10.1093/bioinformatics/btt344
10.1093/bioinformatics/btt344 · External reference
10.1007/s00726-019-02767-6
10.1007/s00726-019-02767-6 · External reference
HH-suite3 for fast remote homology detection and deep protein annotation
10.1186/s12859-019-3019-7 · 2019 · External reference
Protein structural motif prediction in multidimensional ø-ψ space leads to improved secondary structure prediction
10.1089/cmb.2006.13.1489 · 2006 · External reference
Dropout: a simple way to prevent neural networks from overfitting
2014 · External reference
10.1109/bibm.2010.5706547
10.1109/bibm.2010.5706547 · External reference
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10.1038/nbt.3988
10.1038/nbt.3988 · External reference
10.1007/978-1-62703-065-6_5
10.1007/978-1-62703-065-6_5 · 2012 · External reference
Computational prediction of protein secondary structure from sequence
10.1002/cpps.19 · 2016 · External reference
Protein secondary structure prediction: a survey of the state of the art
10.1016/j.jmgm.2017.07.015 · 2017 · External reference
10.1007/978-1-4939-9161-7_4
10.1007/978-1-4939-9161-7_4 · 2019 · External reference
Critical assessment of high-throughput standalone methods for secondary structure prediction
10.1093/bib/bbq088 · 2011 · External reference
Estimation of model accuracy in CASP13
10.1002/prot.25767 · 2019 · External reference
Advances in protein structure prediction and design
10.1038/s41580-019-0163-x · 2019 · External reference
10.1016/s1359-0278(97)00041-2
10.1016/s1359-0278(97)00041-2 · External reference
Reconstruction of 3d Structures From Protein Contact Maps
10.1109/tcbb.2008.27 · 2008 · External reference
The pros and cons of predicting protein contact maps, Methods in Molecular
2008 · External reference
Unit disk graph recognition is NP-hard
10.1016/s0925-7721(97)00014-x · 1998 · External reference
Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins
10.1186/1471-2105-7-402 · 2006 · External reference
Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12
10.1002/prot.25414 · 2018 · External reference
Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3d structure
10.1186/1756-0381-4-1 · 2011 · External reference
Toward an accurate prediction of inter-residue distances in proteins using 2d recursive neural networks
10.1186/1471-2105-15-6 · 2014 · External reference
10.1002/prot.24374
10.1002/prot.24374 · External reference
Predicted residue-residue contacts can help the scoring of 3d models
10.1002/prot.22714 · 2010 · External reference
Beta-sheet prediction using inter-strand residue pairs and refinement with hopfield neural network
1996 · External reference
Unresolved reference
External reference
Three-stage prediction of protein -sheets by neural networks, alignments and graph algorithms
10.1093/bioinformatics/bti1004 · 2005 · External reference
Prediction of disulfide connectivity in proteins
10.1093/bioinformatics/17.10.957 · 2001 · External reference
Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks
10.1093/protein/15.12.951 · 2002 · External reference
DISULFIND: a disulfide bonding state and cysteine connectivity prediction server
10.1093/nar/gkl266 · 2006 · External reference
Improving disulfide connectivity prediction with sequential distance between oxidized cysteines
10.1093/bioinformatics/bti715 · 2005 · External reference
Disulfide connectivity prediction using recursive neural networks and evolutionary information
10.1093/bioinformatics/btg463 · 2004 · External reference
DiANNA: a web server for disulfide connectivity prediction
10.1093/nar/gki412 · 2005 · External reference
A two-stage approach for improved prediction of residue contact maps
10.1186/1471-2105-7-180 · 2006 · External reference
Correlated mutations and residue contacts in proteins
10.1002/prot.340180402 · 1994 · External reference
10.1006/jmbi.1997.1198
10.1006/jmbi.1997.1198 · External reference
10.1093/protein/14.11.835
10.1093/protein/14.11.835 · External reference
Striped sheets and protein contact prediction
10.1093/bioinformatics/bth913 · 2004 · External reference
Improved residue contact prediction using support vector machines and a large feature set
10.1186/1471-2105-8-113 · 2007 · External reference
Improved protein contact predictions with the MetaPSICOV2 server in CASP12
10.1002/prot.25379 · 2018 · External reference
DeepCDpred: inter-residue distance and contact prediction for improved prediction of protein structure
2019 · External reference
10.1371/journal.pcbi.1005324
10.1371/journal.pcbi.1005324 · External reference
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks
10.1093/bioinformatics/btx781 · 2018 · External reference
10.1016/j.cels.2017.11.014
10.1016/j.cels.2017.11.014 · External reference
High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features
10.1093/bioinformatics/bty341 · 2018 · External reference
10.1093/bioinformatics/bty1036
10.1093/bioinformatics/bty1036 · External reference
10.1093/bioinformatics/bty481
10.1093/bioinformatics/bty481 · External reference
Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13
10.1002/prot.25798 · 2019 · External reference
Protein structure prediction using multiple deep neural networks in CASP13
10.1002/prot.25834 · 2019 · External reference
The principled design of large-scale recursive neural network architectures-DAG-RNNs and the protein structure prediction problem
2003 · External reference
NNcon: improved protein contact map prediction using 2d-recursive neural networks
10.1093/nar/gkp305 · 2009 · External reference
Deep architectures for protein contact map prediction
10.1093/bioinformatics/bts475 · 2012 · External reference
Assessment of contact predictions in casp12: co-evolution and deep learning coming of age
10.1002/prot.25407 · 2018 · External reference
10.1093/bioinformatics/btm604
10.1093/bioinformatics/btm604 · External reference
Protein 3d structure computed from evolutionary sequence variation
10.1371/journal.pone.0028766 · 2011 · External reference
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
10.1073/pnas.1111471108 · 2011 · External reference
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
10.1093/bioinformatics/btr638 · 2012 · External reference
FreeContact: fast and free software for protein contact prediction from residue co-evolution
10.1186/1471-2105-15-85 · 2014 · External reference
CCMpred-fast and precise prediction of protein residue-residue contacts from correlated mutations
10.1093/bioinformatics/btu500 · 2014 · External reference
10.1093/bioinformatics/btu791
10.1093/bioinformatics/btu791 · External reference
Critical assessment of methods of protein structure prediction (casp) – round xiii
10.1002/prot.25823 · 2019 · External reference
Assessing the accuracy of contact predictions in casp13
10.1002/prot.25819 · 2019 · External reference
Deep learning
10.1038/nature14539 · 2015 · External reference
10.1002/prot.25697
10.1002/prot.25697 · External reference
Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments
10.1093/bioinformatics/btv592 · 2015 · External reference
Protein multiple sequence alignment benchmarking through secondary structure prediction
10.1093/bioinformatics/btw840 · 2017 · External reference
Quantest2: benchmarking multiple sequence alignments using secondary structure prediction
10.1093/bioinformatics/btz552 · 2020 · External reference
10.1371/journal.pone.0220182
10.1371/journal.pone.0220182 · External reference
Unresolved reference
External reference
End-to-end differentiable learning of protein structure
2019 · External reference
Neural network pairwise interaction fields for protein model quality assessment and ab initio protein folding
10.2174/138920311796957649 · 2011 · External reference
QAcon: single model quality assessment using protein structural and contact information with machine learning techniques
10.1093/bioinformatics/btw694 · 2017 · External reference
10.1038/s42256-019-0075-7
10.1038/s42256-019-0075-7 · External reference
Analysis of several key factors influencing deep learning-based inter-residue contact prediction
2019 · External reference
10.1002/prot.25824
10.1002/prot.25824 · External reference
A further leap of improvement in tertiary structure prediction in casp13 prompts new routes for future assessments
10.1002/prot.25787 · 2019 · External reference
10.1038/nrm3810
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10.1016/j.febslet.2009.06.030
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Pasta 2.0: an improved server for protein aggregation prediction
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